Identifying the environmental cues that determine the timing of developmental processes is vital to understanding the effects of climate change on populations. However, as developmental processes are inherently difficult to measure directly at the population level, the drivers and potential consequences of change in their timings remain unknown in most species. Here we explore the use of long-term monitoring data for assessments of change in the number of generations per year and its impact on abundance, demonstrating new applications for a rapidly growing data source. Data derived from a light trap in west-central Scotland operated over 56 years (1968 to 2023) showed that the small phoenix moth, Ecliptopera silaceata, switched from a univoltine to bivoltine generation pattern. This voltinism change was predicted by an increased minimum temperature in a critical time window towards the later part of the first generation’s flight period. The population shows positive density dependence and the change in voltinism has no significant negative effect on population size, indicating no evidence of a developmental trap that has been postulated for other species. These results identify some of the proximate mechanisms of developmental responses to climate change in general and in voltinism in particular, specifically highlighting the importance of sustained temperature above minimum thresholds for development. These results could also help to make predictions about future changes in population sizes under climate change and increasing voltinism, in addition to how these changes may differ between species.

For migratory species, successful navigation is critical to fitness. In Atlantic salmon, for example, there is evidence that during migration from natal streams to the sea, passage through waters with poorly defined or mixed water velocity patterns may constrain directional navigation, causing individuals to become trapped or delayed in lakes or other bodies with slowly flowing water. In this study, we determined the minimum water velocities needed to elicit a behavioural response, in this case a change in the direction of holding position, in both wild origin and domesticated salmon smolts. Smolts required a directional flow in excess of 8.9 cm s-1 to exhibit effective directional orientation towards the current. Smolts of a domesticated farm origin exhibited a similar qualitative and quantitative response as wild fish. These results suggest that, in areas where the downstream migrating Atlantic salmon smolts pass through low-directional water flow, it may be possible to manipulate directional flows above this minimum threshold, at least temporarily, as a management tool to increase migration success. This is likely to be particularly true where smolts are passing through dams, reservoirs or other impounded waters.

While it is likely that ecological context is important, the factors that facilitate and maintain variable levels of intraspecific diversity in Salmonidae fishes across environments remain unclear. Using a meta-analysis of sympatric ecotype assemblages from two salmonid genera-Salvelinus and Coregonus-we evaluated the importance of ecological factors determining the number of sympatric ecotypes (i.e. 2-7) and the level of trait divergence between them. We found that ecotype diversity increased with lake depth and surface area in both Coregonus and Salvelinus. Further, diversity in Coregonus increased with latitude, while the number of ecotypes in Salvelinus assemblages was linked to climatic seasonality. In comparing the two genera, we found elevated divergence in traits related to ontogeny (i.e. age and body shape) in Salvelinus and gill raker count in Coregonus. Trait divergence in life history traits (i.e. age and body length) in Salvelinus increased with seasonality, whereas contrasting relationships of latitude to body length and gill rakers were found in Coregonus. We also found similar levels of divergence in trait variance in the two genera, suggesting that among-ecotype differences in phenotypic variability are not more common in one genus than the other. Overall, ecosystem characteristics, including lake location, climate and morphometry, are clearly important for where these genera have diversified, but the variables that are most closely associated with intraspecific diversity differ between the two genera studied and depend on whether diversity is quantified using number of ecotypes or trait divergence.

Access to omega-3 long-chain polyunsaturated fatty acids (n-3 LC-PUFA) and habitat complexity have been proposed to influence brain development and cognitive ability. We aimed to investigate the physiological and cognitive effects of dietary n-3 LC-PUFA deprivation on juvenile brown trout (Salmo trutta L.) in complex habitats resembling natal stream conditions in which populations have evolved. We tested effects of n-3 LC-PUFA deficiency in diet and habitat complexity on somatic growth, cognitive performance, encephalization, n-3 LC-PUFA biosynthesis and nutrient routing capacity. Brown trout were raised from egg for 7 months post-hatch on either a high (8.91%) or low (1.79%) n-3 LC-PUFA diet; for the final 3 months, trout were further divided into complex (heavily ornamented tanks with small, dynamic, populations) or simple habitats (bare tanks with many, constant, inhabitants). Recognition, memory and inference were tested by comparing the times required to establish stable hierarchical relationships in agonistic dyadic trials featuring naïve trout and trials in which one of the trout had previously observed the other. Gas chromatography and compound-specific stable hydrogen isotope analysis revealed increased biosynthesis and routing of n-3 LC-PUFA to the brain among trout on n-3 LC-PUFA-deficient diets. Fed to satiation, trout did not sacrifice somatic growth to fuel biosynthesis and routing of n-3 LC-PUFA. However, dietary deficiency in n-3 LC-PUFA did lead to smaller brains, and smaller brains were associated with lower cognitive performance. Complex habitats elicited better cognitive performance, and were associated with lower somatic growth, but habitat complexity played only minor roles in encephalization and the n-3 LC-PUFA composition of brain lipids. We conclude that developmental plasticity in response to environment allows brown trout partially to compensate for the paucity of dietary n-3 LC-PUFA, and we suggest that cognitive divergences may play a role in the diversification of life-history variants among brown trout in the wild.

Elevated temperatures from climate change are predicted to be more extreme at higher latitudes. This could require phenotypic plasticity to generate variation that allows organisms to persist in these regions. However, climate change will provide a multifactorial change in environmental cues, making an understanding of how they interact essential for predicting persistence and future evolutionary potential. Here, the impacts of temperature on ecologically relevant phenotypic plasticity (foraging environment) in Arctic charr (Salvelinus alpinus) were studied. Eggs and alevins were kept at the same temperature (9°C) and split using a factorial design. This included two temperature treatments (10°C and 14°C) and two treatments representing benthic and pelagic foraging styles. We measured morphology in response to these treatment combinations and found an interaction between foraging and temperature-induced plasticity in body shape that included changes in body depth and the caudal peduncle that could impact swimming ability and fitness. This indicates that thermal conditions may change how plasticity responds to ecological conditions and impact adaptive variation.

The role played by omega-3 long-chain polyunsaturated fatty acids (n-3 LC-PUFA) in life-history polymorphisms in partially migratory species remains poorly understood. Yet, brain development is highly dependent upon nutrition, particularly the supply of n-3 LC-PUFA, derived from diet or internally converted from their shorter-chain precursors, and the fitness of animals may be shaped by cognitive performance, including effective spatial navigation required by migration. We investigated juveniles of a wild polymorphic population of brown trout, Salmo trutta , with three distinct migratory ecotypes, at the point of first outward migration. Using a combination of fatty acid contents, compound-specific stable isotope analysis, and liver transcriptomics, we found that non-migrants compensated for dietary deficiency by biosynthesising n-3 LC-PUFA from precursor molecules and routing them to cell membranes to a greater extent than did migrants. These findings highlight contrasting intake and processing between migratory and non-migratory life histories of nutrients associated with brain development. ### Competing Interest Statement The authors have declared no competing interest. Natural Environment Research Council, https://ror.org/02b5d8509, NR/W008963/1 Leverhulme Trust, https://ror.org/012mzw131, ECF-2020-509 FWF Austrian Science Fund, https://ror.org/013tf3c58, 10.55776/P35515 Fisheries Society of the British Isles, https://ror.org/00q2kx914

Defining appropriate conservation units is crucial to the protection and management of biodiversity. These delineations deliver further benefit when they include assessments of population vulnerability to extinction from pressures such as climate change. However, delineations and vulnerability assessments are particularly difficult within highly diverse species, such as the salmonid fish Arctic charr (Salvelinus alpinus), that show extensive phenotypic and genetic variation within and across locations, variable and complex life histories and broad geographic distributions. As yet, the nature and scope of Arctic charr diversity has not been characterised at the scale needed to delineate key conservation units in Scotland. To identify evolutionarily significant and vulnerable populations to prioritise for conservation, we conducted a genomic study of Arctic charr populations across Britain and Ireland with a focus on Scottish populations (N = 64 populations; 24,878 SNPs; 410 individuals). We found that most lake populations represented distinct genetic clusters, with limited gene flow between them and resulting in substantial genetic differentiation. Higher level groupings of genetic similarity across catchments likely reflect historic anadromy and migration, with populations primarily grouping east or west of the central watershed divide in Scotland. Analysing genetic offset, also known as genomic vulnerability, we identified strong inverse correlations between genetic vulnerability and latitude and distance to the sea, suggesting that more southern and more inland populations are more vulnerable to the effects of climate change. Additionally, patterns of vulnerability across several additional metrics identified other populations that may be at higher risk of loss. We further used our genetic data, along with phenotypic and geographic information, to identify populations of greatest evolutionary significance. This highlighted that the most important ones to protect are those in locations with multiple ecotypes, a key facet of functional Arctic charr biodiversity, and populations that are the only ones in their Hydrometric Area.

Migration is a high-risk behavior. For the Atlantic salmon, Salmo salar, migrating from its river nursery area to marine feeding grounds, the magnitude of risk varies with habitat type. Passage through lakes, in particular, is associated with low rates of migration success. Downstream migrating salmon smolts are rheotactic when migrating in rivers, but lakes typically provide poorer directional currents for migrating salmon. In this study we tested if, in the absence of clear navigational cues in lakes, Atlantic salmon smolts switch to a random search strategy to find the outflowing river. We constructed random search simulations to test if lake basin shape has an effect on migration success. We also compared simulated migration characteristics with migrations of salmon smolts through five real lakes for which there are telemetry data for migrating salmon. Correlated random walk simulations showed that a random search strategy could be successful for all lake shapes tested but was more successful in curved (round and elliptical) than rectangular basin shapes. Rectangular basins with the migration start and stop points at the ends of the lake had a higher success than those where these points were perpendicular to the axis of the lake. In general, a random walk model predicted the migration success rate of fish tracked through real lakes. However, for two lakes the simulated migration success exceeded that of actual success, suggesting that fish passing through these lakes were not adopting a random search strategy. We speculate that this is the result of either conflicting navigational cues which inhibit smolts from finding the lake outlet or that they temporarily suspend migration (e.g., to feed). Modelling predicted that for small lakes, directional swimming in short steps (ca. 100 m) followed by turns with very low variation from the direction of travel resulted in the highest migration success. For larger lakes, longer step lengths but also with low turn variation (simulated turning angle drawn from distributions of standard deviation 2° and 5° around a mean of 0°) resulted in the highest migration success. We conclude that navigation in downstream migrating salmon smolts switches from rheotaxis in rivers to a random search tactic in lakes except where residual flow cues in some lakes prevent this, at times resulting in suboptimal navigation outcomes.

The migratory behavior of Atlantic salmon (Salmo salar) post-smolts in coastal waters is poorly understood. In this collaborative study, 1914 smolts, from 25 rivers, in four countries were tagged with acoustic transmitters during a single seasonal migration. In total, 1105 post-smolts entered the marine study areas and 438 (39.6%) were detected on a network of 414 marine acoustic receivers and an autonomous underwater vehicle. Migration pathways (defined as the shortest distance between two detections) of up to 575 km and over 100 days at sea were described for all 25 populations. Post-smolts from different rivers, as well as individuals from the same river, used different pathways in coastal waters. Although difficult to generalize to all rivers, at least during the year of this study, no tagged post-smolts from rivers draining into the Irish Sea were detected entering the areas of sea between the Hebrides and mainland Scotland, which is associated with a high density of finfish aquaculture. An important outcome of this study is that a high proportion of post-smolts crossed through multiple legislative jurisdictions and boundaries during their migration. This study provides the basis for spatially explicit assessment of the impact risk of coastal pressures on salmon during their first migration to sea.

Riverine habitat fragmentation by barriers, including impoundments, is common and their effects on obligate aquatic organisms are manifold. Organisms, such as Atlantic salmon (Salmo salar), that make extensive river migrations are particularly vulnerable to the effects of impoundments. In this study, we use acoustic telemetry to examine the migratory behaviour of Atlantic salmon, as they migrate to sea for the first time as juvenile 'smolts', in a river with a series of dams that form a complex hydropower scheme. We demonstrate that overall migration success in the River Dee catchment and particularly through standing waters was remarkably high. We speculate that high migration success in standing waters could be due to relative current speeds providing good quality directional cues to migrants. Migration success past the two dams in this study, was relatively high, although the number of unsuccessful passage attempts before a successful passage was also very high. The vast majority of smolts passed the dams when the turbines were operational. At one dam, smolts did not use an available fish pass but migrated through the generating turbines. These findings provide several routes through which generation could be managed to enhance the success of downstream smolt migration in rivers where there are similar patterns of hydrogeneration in place.

Abstract Understanding the extrinsic factors that drive the emergence of biological diversity is critical to its protection and management. However, even superficially similar local environments can vary considerably, and so large-scale datasets are needed to understand the key drivers across a representative portion of a species distribution. Arctic charr (Salvelinus alpinus) is a widespread salmonid fish that represents an excellent study system for these processes because the species shows substantial diversification to a range of freshwater environments and multiple instances of trophic specialization in the form of sympatric ecotype populations. However, the processes behind this variation remain largely unknown due to a lack of broad-scale studies. To address this, we investigated the drivers of diversity via a national-scale study of 64 Arctic charr populations in lakes across Scotland using a genome-wide dataset of single nucleotide polymorphisms (N = 24 878) and phenotypic data of head depth relative to body size. We found that the extent of genetic and phenotypic diversity was predicted by ecosystem size (a proxy of lake size, depth, and complexity). We suggest this is because larger, deeper lakes generally provided more ecological opportunity and diversification potential. Additionally, using environmental data from all 187 lakes containing Arctic charr in Scotland, we found that ecosystem size strongly predicted the potential for trophic specialization and the presence of sympatric divergent ecotypes. Our results show the importance of ecological opportunity in underlying adaptive radiations.

Global freshwater biodiversity has witnessed a decline of over 80% since the 1970s, with freshwater mussel fauna exhibiting some of the highest extinction rates of any group of organisms globally. The quantification and assessment of dynamic hydrogeomorphological processes is crucial in defining suitable habitat for aquatic benthic species. Yet a consistent approach to accurately record and monitor near-bed flow characteristics, remains largely undefined in freshwater ecology. The purpose of this proof-of-concept work was to provide a direct, non-intrusive, low-cost and accessible tool to evaluate near-bed incipient flow conditions and predict when flow forcing results in the entrainment of individual benthic species. This study designed, for the first time, an instrumented freshwater mussel, encompassing inertial microelectromechanical sensors (MEMS), housed within Freshwater Pearl Mussel (Margaritifera margaritifera) shells. Following initial calibration of the sensors, flume experiments were undertaken to assess instrumented shell movement metrics, for a range of flow conditions and shell orientations. Analysis found the biosensors could successfully detect, and potentially predict, entrainment events through the examination of variability in recordings of total acceleration, with entrainment risk shown to vary across flow-rate, shell orientation and size. The biosensor could provide a valuable tool for assisting conservation management of freshwater species: assisting in habitat suitability surveys and aiding identification and monitoring of suitable habitat in reintroduction and restoration schemes.

Tracking of animal migrations using telemetry technologies needs to take into consideration the burden that the tag exerts on the animal. Here, we examined the potential impacts of acoustic tags of two sizes (nominally a 'V6' [smaller] and 'V7' [larger]) on the downstream riverine migration success and behaviour of wild Atlantic salmon (Salmo salar L.) smolts. One hundred fish were tagged with either a V6 or V7 tag. Tag burden (tag: fish weight) ranged from 1.88% to 7.39% and differed significantly between fish tagged with the V6 (mean [SD] = 3.63% [0.51%]) and the V7 tags (mean [SD] = 5.84% [0.95%]). There was no significant difference in the in-river migration failure between the two groups when tested with a time-to-event analysis. There were also no differences in other elements of the migratory behaviour (rate of movement, time of detection and residency time) between the two tagging groups. These data support the use of acoustic tracking for monitoring smolt migration and highlight that tagging of smaller smolts at up to 7.39% tag burden to gain a more representative understanding of migration success and behaviours across a smolt population.

Acoustic telemetry can provide valuable space-use data for a range of marine species. Yet the deployment of species-specific arrays over vast areas to gather data on highly migratory vertebrates poses formidable challenges, often rendering it impractical. To address this issue, we pioneered the use of acoustic telemetry on basking sharks (Cetorhinus maximus) to test the feasibility of using broadscale, multi-project acoustic receiver arrays to track the movements of this species of high conservation concern through the coastal waters of Ireland, Northern Ireland, and Scotland. Throughout 2021 and 2022, we tagged 35 basking sharks with acoustic transmitters off the west coast of Ireland; 27 of these were detected by 96 receiver stations throughout the study area (n = 9 arrays) with up to 216 detections of an individual shark (mean = 84, s.d. 65). On average, sharks spent 1 day at each acoustic array, with discrete residency periods of up to nine days. Twenty-one sharks were detected at multiple arrays with evidence of inter-annual site fidelity, with the same individuals returning to the same locations in Ireland and Scotland over 2 years. Eight pairs of sharks were detected within 24 h of each other at consecutive arrays, suggesting some level of social coordination and synchronised movement. These findings demonstrate how multi-project acoustic telemetry can support international, cost-effective monitoring of basking sharks and other highly mobile species. Decision support tools such as these can consolidate cross-border management strategies, but to achieve this goal, collaborative efforts across jurisdictions are necessary to establish the required infrastructure and secure ongoing support.

Migratory species typically undertake demanding long-distance journeys, across different habitat types during which they are exposed to multiple natural and anthropogenic stressors. Mortality during migration is typically high and may be human induced. Understanding individual responses to these selection pressures is rarely attempted because of the challenges of relating individual phenotypic and genetic data to migration success. Here, we show distinct single nucleotide polymorphism (SNP) sets significantly differentiated between Atlantic salmon smolts making successful migrations to sea and those that failed to migrate, in two different rivers. In contrast, morphological variation was not diagnostic of migration success. Populations from each river were genetically distinct, and while different genes were possibly implicated in migration success in each river, they related to common biological processes (e.g., osmoregulation and immune and stress response). Given that migration failure should quickly purge polymorphism at selected SNPs from a population, the question of how genetic diversity in these populations is maintained is an important one. Standing genetic variation could be maintained by different life history strategies and/or environmentally driven balancing selection. Our work highlights the importance of preserving genetic diversity to ensure evolutionary resilience at the population level and has practical implications for management.

There is some evidence that the river migration success of Atlantic salmon smolts, on their first migration to sea, varies both spatially and temporally. However, we have only a poor understanding of what may be driving this variation. In this study, we used acoustic telemetry to quantify the spatial and temporal variations in river migration success in Atlantic salmon smolts on their first migration to sea. In total 4120 Atlantic salmon smolts migrating through 22 rivers in Scotland, England, Ireland, and Northern Ireland over multiple years were included in the study. Individuals were defined as successful migrants if detected leaving the river to enter marine waters. The results show significant temporal (up to 4 years) and spatial (river) variations in migration success, with overall between-river migration success varying from 3.4% to 97.0% and between years from 3.4% and 61.0%. Temporal variation in migration success was river specific, with some rivers being more temporally stable (exhibiting little variation between years) than others. Across all rivers and years, individual migration success was predicted positively by body condition and negatively by tag burden. The rate of migration success for a population (migration success standardized to a common river distance [proportion km-1]) was predicted by a number of environmental factors. The proportion of river catchment that comprised wetland and woodland positively predicted migration success, whereas the proportion of grassland and peatland in a catchment negatively predicted the rate of migration success. Although the mechanisms through which these effects may be operating were not directly examined in this study, we discuss some potential routes through which they may occur.

Across its Holarctic range, Arctic charr (Salvelinus alpinus) populations have diverged into distinct trophic specialists across independent replicate lakes. The major aspect of divergence between ecomorphs is in head shape and body shape, which are ecomorphological traits reflecting niche use. However, whether the genomic underpinnings of these parallel divergences are consistent across replicates was unknown but key for resolving the substrate of parallel evolution. We investigated the genomic basis of head shape and body shape morphology across four benthivore-planktivore ecomorph pairs of Arctic charr in Scotland. Through genome-wide association analyses, we found genomic regions associated with head shape (89 SNPs) or body shape (180 SNPs) separately and 50 of these SNPs were strongly associated with both body and head shape morphology. For each trait separately, only a small number of SNPs were shared across all ecomorph pairs (3 SNPs for head shape and 10 SNPs for body shape). Signs of selection on the associated genomic regions varied across pairs, consistent with evolutionary demography differing considerably across lakes. Using a comprehensive database of salmonid QTLs newly augmented and mapped to a charr genome, we found several of the head and body shape associated SNPs were within or near morphology QTLs from other salmonid species, reflecting a shared genetic basis for these phenotypes across species. Overall, our results demonstrate how parallel ecotype divergences can have both population-specific and deeply shared genomic underpinnings across replicates, influenced by differences in their environments and demographic histories.

Untangling the patterns and proximate drivers of intraspecific genetic and phenotypic structuring informs our understanding of the evolutionary processes shaping diversity. This study investigated morphological and genetic structuring of brown trout (Salmo trutta L.) populations across varying spatial scales in a single, complex, dendritic river catchment and examined the potential natural and anthropogenic environmental features driving this structuring. Morphometric and hierarchical genetic structuring analyses of fish from 22 sampling sites in the River Foyle catchment, Ireland ( 4500km2) identified 19 morphologically distinct groups and 15 genetically distinct populations, separated by river distances ranging from 0.4 km to 188 km. Isolation by Distance was the main factor shaping both genetic and morphological divergence, indicating that strong philopatry is one of the major drivers of the observed population structuring in this system. However, both natural and anthropogenic environmental variables also explained pairwise genetic and morphological differences between sampling sites. Thus, the pairwise differences in the area of woodland in the upstream catchment, water phosphorus concentration, biological oxygen demand, catchment slope, urban area in upstream catchment, altitude, site specific percentage of canopy cover and dissolved oxygen concentration in the river channel were correlated with genetic divergence. The pairwise differences in the concentration of suspended solids, the extent of bankside overhang, the composition of bedrock, boulder and cobble substrates, watercourse width, catchment slope and site altitude were correlated with between-site morphological differences. We hypothesise that local differential selection pressures comprising both natural environmental variation and variation resulting from anthropogenic effects, in combination with strong philopatry and random genetic processes drive the clearly defined genetic and phenotypic patterns described here.

Trap and transport, the capture and subsequent translocation of fish during the freshwater phase of their migration, is becoming more common as a management intervention. Although the technique can be successful, it is costly and can have unintended effects on the fish being transported. This study investigates whether trap and transport can be used to increase the migration success of Atlantic salmon, Salmo salar, smolts in naturally flowing rivers. Seaward-migrating S. salar (n = 294) from two UK rivers were tracked using acoustic telemetric techniques. Outmigration success and timing were compared between non-transported (released at the original in-river capture site) and transported (released ca. 23 km downstream of the capture site) individuals. Downstream translocation increased the proportion of fish that successfully migrated to marine waters, and there was no indication that transport reduced post-release survival. The post-release migration speed of transported fish was slower than expected but this was likely a function of their advanced migration timing rather than an inhibition of their capacity to migrate. These results suggest that trap and transport can increase the outmigration success of S. salar smolts, but the earlier river exit dates of transported fish could negatively affect their survival at sea.

Conflicts can arise in developmental pathways that prevent an individual entering different developmental life stages that result in the expression of different phenotypes within a specific time period. In salmonids, theory suggests that sexual maturation may inhibit subsequent smolting within the same 12-month period and that this is partly the result of the time and the apparently conflicting physiological changes for these processes to occur, and partly because of the energy requirements for these physiologically taxing processes. This study tested whether sexually mature male Atlantic salmon (Salmo salar L.) parr, caught in the autumn, would subsequently smolt the following spring. Through individual identification using PIT telemetry, minimum estimates of 3.0% (n = 6/203) and 5.9% (n = 1/17) of Atlantic salmon parr that were sexually mature in two river catchments during the autumn were subsequently identified as smolts in the following spring. We therefore suggest that, in line with previous studies on domesticated Atlantic salmon and laboratory-based experiments, there is no developmental conflict but that life-history expression is mediated by environmental and genetic processes.